Stewart Talbot's goal ended Hinckley's brave FA Cup run and set up a third round tie against Luton Town.
The Bees were held goalless until the 52nd minute when Hinckley's Brad Piercewright handled in the area and Alex Rhodes scored from the spot.
Piercewright was red carded but the plucky non-league side equalised five minutes later when Richard Lavery converted a Jamie Lenton free-kick.
But Talbot took advantage of some slack defending to race away for the winner.
Brentford dominated the opening 45 minutes of the second round replay and could have taken the lead after five minutes.
But Rhodes was denied a simple tap in by the first of a series of fine saves from Hinckley keeper Thomas Whittle.
The experienced campaigner John Salako then set up Jay Tabb to head just wide and Chris Hargreaves drilled a shot just off target.
Nationwide North side Hinckley made it to half-time on level terms.
But three goals in seven minutes after the break brought the tie to life.
Brentford struck first when Piercewright had no option but to use his hand to tip a shot over the bar.
That ended his involvement in the game and Rhodes kept his cool to send the keeper the wrong way with the resulting spot-kick.
Despite being down to 10 men Hinckley got a leveller through Lavery before Talbot restored the League One side's advantage.
Ben May twice went close to adding to Brentford's lead with a downward header and a shot on the turn, but Whittle was equal to both efforts.
Hinckley came within inches of forcing extra-time, but Wayne Dyer's effort slipped just wide of the target.
Brentford travel to League One leaders Luton in the third round in January.
Brentford: Nelson, O'Connor, Sodje, Myers, Salako, Tabb, Talbot (Hutchinson 90.00), Hargreaves, Rhodes,
May (Harrold 85.00), Burton (Rankin 63.00).
Subs Not Used: Julian, Osborne.
Goals: Rhodes 52 pen, Talbot 59.
Hinckley Utd: Whittle, Willis, Storer (Goodwin 82.00),
Piercewright, Cartwright, Lavery, Dyer, Burns (McMahon 78.00),
Lenton, Lewis, Barnes (Marrison 68.00).
Subs Not Used: Pitham, Di Gregorio.
Sent Off: Piercewright (51).
Goals: Lavery 57.
Ref: Phil Crossley (Bromley).